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BioSequenceModify
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BioSequenceModify

[Experimental]

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BioSequenceModify[seq,"mod"]

gives the result of applying the modification "mod" to the sequence seq.

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BioSequenceModify[seq,{"mod",params}]

specifies the parameters params for "mod".

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represents an operator form of BioSequenceModify that can be applied to a biomolecular sequence.

Details

  • Bond modifications:
  • {"AddBond",{i1,i2}}add a higher-order bond between letters at i1 and i2
    {"AddBond",Bond[{i1,i2},"type"]}add a bond of the given type between the given indices
    {"DeleteBond",{i1,i2}}remove all higher-order bonds between the given indices
    {"DeleteBond",Bond[{i1,i2},"type"]}remove the specified bond between the given indices
  • Circularity adjustment modifications:
  • "MakeCircular"convert a linear sequence into a circular sequence
    "MakeLinear"convert a circular sequence into a linear sequence
    {"MakeLinear",i}convert to a linear sequence, starting at the i^(th) position
  • Collection modifications:
  • {"AddToCollection",{seq1,seq2,…}}incorporate a list of sequences into a sequence collection
    "SplitDisconnectedCollection"separate unbonded clusters into separate collections
  • Representation-only modifications:
  • "InnermostBondRepresentation"represent bonds at the innermost applicable sequence
    "OutermostBondRepresentation"represent bonds at the outermost sequence
    "CanonicalRepresentation"convert all sequences and bonds to a canonical form
  • Translation modifications:
  • "DropIncompleteCodons"drop incomplete codons from the end of DNA or RNA
    "DropToStartCodon"drop letters from DNA or RNA until a start codon is found
    "DropFromStopLetter"drop the letters from a peptide after a stop letter is found

Examples

open allclose all

Basic Examples  (12)Summary of the most common use cases

Add a bond to a sequence:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-3d5rmr
Out[1]=1

Delete a bond from a sequence:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-jdgraf
Out[1]=1

Represent all bonds at the innermost sequence, with all letters included:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-russbw

Represent all bonds at the outermost sequence:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-6lp7g6

Canonicalize the representation of bonds and sequences into a sorted and reduced form:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-q5q6gz

Convert a linear sequence to a circular sequence:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-4eu9i7
Out[1]=1

Convert a circular sequence to a linear sequence:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-dcjuuh
Out[1]=1

Add a list of sequences into a sequence collection:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-gxuqil
Out[1]=1

Separate the unbound components of a sequence collection into separate collections:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-3twyki
Out[1]=1

Drop letters at the end of a nucleotide sequence so only complete codons are present for translation:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-h06cnf
Out[1]=1

Drop the letters up to a start codon in the default genetic translation table:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-uux46f
Out[1]=1

Drop terms after the stop letter in a peptide sequence:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-lgjgsz
Out[1]=1

Scope  (23)Survey of the scope of standard use cases

"AddBond"  (4)

A bond type does not need to be specified to insert a bond. If one is not given, it will be inferred:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-6eg7n
In[2]:=2
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https://wolfram.com/xid/0c0rop47925i0-8ps7dj
Out[2]=2

The type of the bond inferred may depend on the letters being linked:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-8ipf3g
In[2]:=2
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https://wolfram.com/xid/0c0rop47925i0-wgwdns

Bonds can be added to hybrid strands:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-xge3ai
Out[1]=1
In[2]:=2
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https://wolfram.com/xid/0c0rop47925i0-gleai2
Out[2]=2

Bonds can be added to sequence collections:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-2dmffo
Out[1]=1
In[2]:=2
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https://wolfram.com/xid/0c0rop47925i0-cm7odz
Out[2]=2

"AddToCollection"  (3)

A single sequence can also be added to a collection:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-n7k839

A single motif or hybrid sequence will be modified into a collection:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-ym4yn6
Out[1]=1

If there are multiple sequence collections, they will be merged in the result:

In[1]:=1
✖
https://wolfram.com/xid/0c0rop47925i0-fhiklb
Out[1]=1

"CanonicalRepresentation"  (3)

If sequences are identical, canonicalization will use strand-level bonds for ordering:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-qhlkrx
Out[1]=1

If the sequences and strand-level bonds are identical, canonicalization will use sequence bonds for ordering:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-ml6xai
Out[1]=1

In addition to sorting, single-strand collections are reduced to the strand and single motif hybrids are reduced to the motif:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-4u36jg
Out[1]=1

"DeleteBond"  (2)

Delete all higher-order bonds between the two indexes:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-5hsgv0
Out[1]=1

Deleting bonds always works on the outermost form, which is the form given by the "SequenceBondList" property:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-j91axq
Out[1]=1
In[2]:=2
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https://wolfram.com/xid/0c0rop47925i0-d4ojrn
Out[2]=2
In[3]:=3
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https://wolfram.com/xid/0c0rop47925i0-uta0h8
Out[3]=3

"DropToStartCodon"  (3)

Any genetic translation table entity can be used to specify start codons:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-za3w73
Out[1]=1

A specific codon or list of codons can be used as the start codon specification:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-qey558
Out[1]=1
In[2]:=2
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https://wolfram.com/xid/0c0rop47925i0-i56qrd
Out[2]=2

Modifications can be created in an operator form for later use:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-tfn1i
Out[1]=1

Modifications with further specifications can also be used in operator form:

In[2]:=2
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https://wolfram.com/xid/0c0rop47925i0-k42v01
Out[2]=2

"InnermostBondRepresentation"  (1)

Moving bonds inward can potentially bring them into the motif from several layers:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-r8jmcm

"MakeCircular"  (2)

RNA sequences can be converted to circular RNA sequences:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-gceh7u
Out[1]=1

Peptide sequences can be converted to circular peptide sequences:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-davy1y
Out[1]=1

"MakeLinear"  (3)

Circular RNA sequences can be converted to linear RNA sequences:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-5b7rzb
Out[1]=1

Circular peptide sequences can be converted to linear peptide sequences:

In[1]:=1
✖
https://wolfram.com/xid/0c0rop47925i0-xqhc89
Out[1]=1

Start the linear sequence from a specific position:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-rlaqs
Out[1]=1

Relative bond positions are preserved when converting circular sequences to linear sequences:

In[2]:=2
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https://wolfram.com/xid/0c0rop47925i0-jp6b2y

"OutermostBondRepresentation"  (1)

Moving bonds inward will bring them from inside any motif or strand to the outermost sequence structure:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-gdf6vo

"SplitDisconnectedCollection"  (1)

Splitting connections will renumber bonds based on new collection memberships:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-ld2ucf
Out[1]=1

Applications  (1)Sample problems that can be solved with this function

A circular peptide:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-kd2wrs

Various peptides can be related to each other through a circular permutation:

In[2]:=2
✖
https://wolfram.com/xid/0c0rop47925i0-gh3w5d
Out[2]=2
In[3]:=3
✖
https://wolfram.com/xid/0c0rop47925i0-wx6l5
Out[3]=3
In[4]:=4
✖
https://wolfram.com/xid/0c0rop47925i0-bmunen
Out[4]=4
In[5]:=5
✖
https://wolfram.com/xid/0c0rop47925i0-julvqd
Out[5]=5
In[6]:=6
✖
https://wolfram.com/xid/0c0rop47925i0-j7xxc1
Out[6]=6
In[7]:=7
✖
https://wolfram.com/xid/0c0rop47925i0-ktpd7h
Out[7]=7

Possible Issues  (2)Common pitfalls and unexpected behavior

A given modification may not apply to a particular type of sequence:

In[1]:=1
✖
https://wolfram.com/xid/0c0rop47925i0-z9021x
Out[1]=1

If a bond type cannot be inferred, an untyped bond is added:

In[1]:=1
✖
https://wolfram.com/xid/0c0rop47925i0-zf5yd3

Neat Examples  (1)Surprising or curious use cases

Represent the protein preproinsulin as a BioSequence:

In[1]:=1
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https://wolfram.com/xid/0c0rop47925i0-e5yc2o

Remove the signal peptide sequence to make proinsulin:

In[2]:=2
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https://wolfram.com/xid/0c0rop47925i0-d92i6z
Out[2]=2

Add the disulfide bonds and split the proinsulin sequence to make insulin:

In[3]:=3
✖
https://wolfram.com/xid/0c0rop47925i0-dymanb
Out[3]=3
✖
https://wolfram.com/xid/0c0rop47925i0-bav907
Out[14]=14
Wolfram Research (2020), BioSequenceModify, Wolfram Language function, https://reference.wolfram.com/language/ref/BioSequenceModify.html (updated 2021).
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Wolfram Research (2020), BioSequenceModify, Wolfram Language function, https://reference.wolfram.com/language/ref/BioSequenceModify.html (updated 2021).

Text

Wolfram Research (2020), BioSequenceModify, Wolfram Language function, https://reference.wolfram.com/language/ref/BioSequenceModify.html (updated 2021).

✖
Wolfram Research (2020), BioSequenceModify, Wolfram Language function, https://reference.wolfram.com/language/ref/BioSequenceModify.html (updated 2021).

CMS

Wolfram Language. 2020. "BioSequenceModify." Wolfram Language & System Documentation Center. Wolfram Research. Last Modified 2021. https://reference.wolfram.com/language/ref/BioSequenceModify.html.

✖
Wolfram Language. 2020. "BioSequenceModify." Wolfram Language & System Documentation Center. Wolfram Research. Last Modified 2021. https://reference.wolfram.com/language/ref/BioSequenceModify.html.

APA

Wolfram Language. (2020). BioSequenceModify. Wolfram Language & System Documentation Center. Retrieved from https://reference.wolfram.com/language/ref/BioSequenceModify.html

✖
Wolfram Language. (2020). BioSequenceModify. Wolfram Language & System Documentation Center. Retrieved from https://reference.wolfram.com/language/ref/BioSequenceModify.html

BibTeX

@misc{reference.wolfram_2025_biosequencemodify, author="Wolfram Research", title="{BioSequenceModify}", year="2021", howpublished="\url{https://reference.wolfram.com/language/ref/BioSequenceModify.html}", note=[Accessed: 19-June-2025 ]}

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@misc{reference.wolfram_2025_biosequencemodify, author="Wolfram Research", title="{BioSequenceModify}", year="2021", howpublished="\url{https://reference.wolfram.com/language/ref/BioSequenceModify.html}", note=[Accessed: 19-June-2025 ]}

BibLaTeX

@online{reference.wolfram_2025_biosequencemodify, organization={Wolfram Research}, title={BioSequenceModify}, year={2021}, url={https://reference.wolfram.com/language/ref/BioSequenceModify.html}, note=[Accessed: 19-June-2025 ]}

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@online{reference.wolfram_2025_biosequencemodify, organization={Wolfram Research}, title={BioSequenceModify}, year={2021}, url={https://reference.wolfram.com/language/ref/BioSequenceModify.html}, note=[Accessed: 19-June-2025 ]}